Definitely cut both at once so as to match the angles.
The way I did mine was with a circular saw sled. Just a strip of plywood, however long you want it to be, with a fence on one edge to guide the edge of the baseplate on the saw. Make the strip a little wide, so that the first time you run the saw down the length of it, the cut line will be established. So long as you are using the same saw and blade, the cut line will always be right where the edge of the plywood is.
In use, you put the sled on top of the work, line up the cut line where you want it, and clamp it in place. The fence guides the saw, and your cut goes right where you wanted it to.
The only tricky part of this is clamping the sled to a couple of little skinny pieces of stock like you'e make rub rails out of and not have the sled rock around all over the place. Cutting two pieces of stock at once will help, or better yet all four, if your sled is long enough. You can also put scrap pieces that are the same thickness as your stock under the sled to support it, if that helps.
What I'm calling a "sled" might also be called a "shooting board". I'll try to post a picture of mine later when I get a chance. Some of this babble might seem a lot more obvious when you see the device.
George